如何在费希尔-赖特突变选择框架下计算蛋白质编码基因的非同义与同义比率。
How to calculate the non-synonymous to synonymous rate ratio of protein-coding genes under the Fisher-Wright mutation-selection framework.
作者信息
Dos Reis Mario
机构信息
Department of Genetics, Evolution and Environment, University College London, Gower Street, London WC1E 6BT, UK
出版信息
Biol Lett. 2015 Apr;11(4):20141031. doi: 10.1098/rsbl.2014.1031.
Abstract
First principles of population genetics are used to obtain formulae relating the non-synonymous to synonymous substitution rate ratio to the selection coefficients acting at codon sites in protein-coding genes. Two theoretical cases are discussed and two examples from real data (a chloroplast gene and a virus polymerase) are given. The formulae give much insight into the dynamics of non-synonymous substitutions and may inform the development of methods to detect adaptive evolution.
摘要
群体遗传学的基本原理被用于推导公式，这些公式将非同义替换率与同义替换率的比值，与作用于蛋白质编码基因密码子位点的选择系数联系起来。文中讨论了两种理论情况，并给出了两个来自实际数据的例子（一个叶绿体基因和一个病毒聚合酶）。这些公式为非同义替换的动态变化提供了深入见解，并可能为检测适应性进化的方法的发展提供参考。
相似文献
1
How to calculate the non-synonymous to synonymous rate ratio of protein-coding genes under the Fisher-Wright mutation-selection framework.
Biol Lett. 2015 Apr;11(4):20141031. doi: 10.1098/rsbl.2014.1031.
2
Whole-gene positive selection, elevated synonymous substitution rates, duplication, and indel evolution of the chloroplast clpP1 gene.
PLoS One. 2008 Jan 2;3(1):e1386. doi: 10.1371/journal.pone.0001386.
3
Relative rates of synonymous substitutions in the mitochondrial, chloroplast and nuclear genomes of seed plants.
Mol Phylogenet Evol. 2008 Dec;49(3):827-31. doi: 10.1016/j.ympev.2008.09.009. Epub 2008 Sep 21.
4
A beginners guide to estimating the non-synonymous to synonymous rate ratio of all protein-coding genes in a genome.
Methods Mol Biol. 2015;1201:65-90. doi: 10.1007/978-1-4939-1438-8_4.
5
Detecting Adaptation in Protein-Coding Genes Using a Bayesian Site-Heterogeneous Mutation-Selection Codon Substitution Model.
Mol Biol Evol. 2017 Jan;34(1):204-214. doi: 10.1093/molbev/msw220. Epub 2016 Oct 15.
6
A combined empirical and mechanistic codon model.
Mol Biol Evol. 2007 Feb;24(2):388-97. doi: 10.1093/molbev/msl175. Epub 2006 Nov 16.
7
Selective pressures at a codon-level predict deleterious mutations in human disease genes.
J Mol Biol. 2006 May 19;358(5):1390-404. doi: 10.1016/j.jmb.2006.02.067. Epub 2006 Mar 15.
8
Codon usage and selection on proteins.
J Mol Evol. 2006 Nov;63(5):635-53. doi: 10.1007/s00239-005-0233-x. Epub 2006 Oct 14.
9
Large-scale analyses of synonymous substitution rates can be sensitive to assumptions about the process of mutation.
Gene. 2006 Aug 15;378:58-64. doi: 10.1016/j.gene.2006.04.024. Epub 2006 May 22.
10
Molecular evolution of synonymous codon usage in Populus.
BMC Evol Biol. 2008 Nov 4;8:307. doi: 10.1186/1471-2148-8-307.
引用本文的文献
1
Estimating the proportion of beneficial mutations that are not adaptive in mammals.
PLoS Genet. 2024 Dec 26;20(12):e1011536. doi: 10.1371/journal.pgen.1011536. eCollection 2024 Dec.
2
Complete Chloroplast Genome of and Comparative Analysis with Related Species from Brassicaceae.
Genes (Basel). 2024 Jul 5;15(7):886. doi: 10.3390/genes15070886.
3
Extinction scenarios in evolutionary processes: a multinomial Wright-Fisher approach.
J Math Biol. 2023 Sep 26;87(4):63. doi: 10.1007/s00285-023-01993-7.
4
Molecular evolution and phylogenomic analysis of complete chloroplast genomes of (Anacardiaceae).
Ecol Evol. 2023 May 29;13(5):e10134. doi: 10.1002/ece3.10134. eCollection 2023 May.
5
Comparative and phylogenetic analysis of the complete chloroplast genomes of six Polygonatum species (Asparagaceae).
Sci Rep. 2023 May 4;13(1):7237. doi: 10.1038/s41598-023-34083-1.
6
Next-generation development and application of codon model in evolution.
Front Genet. 2023 Jan 27;14:1091575. doi: 10.3389/fgene.2023.1091575. eCollection 2023.
7
Evolution of Amino Acid Propensities under Stability-Mediated Epistasis.
Mol Biol Evol. 2022 Mar 2;39(3). doi: 10.1093/molbev/msac030.
8
An Improved Codon Modeling Approach for Accurate Estimation of the Mutation Bias.
Mol Biol Evol. 2022 Feb 3;39(2). doi: 10.1093/molbev/msac005.
9
A Mutation-Selection Model of Protein Evolution under Persistent Positive Selection.
Mol Biol Evol. 2022 Jan 7;39(1). doi: 10.1093/molbev/msab309.
10
Dietary Diversification and Specialization in Neotropical Bats Facilitated by Early Molecular Evolution.
Mol Biol Evol. 2021 Aug 23;38(9):3864-3883. doi: 10.1093/molbev/msab028.
本文引用的文献
1
The relationship between dN/dS and scaled selection coefficients.
Mol Biol Evol. 2015 Apr;32(4):1097-108. doi: 10.1093/molbev/msv003. Epub 2015 Jan 8.
2
A penalized-likelihood method to estimate the distribution of selection coefficients from phylogenetic data.
Genetics. 2014 May;197(1):257-71. doi: 10.1534/genetics.114.162263. Epub 2014 Feb 14.
3
Estimating the distribution of selection coefficients from phylogenetic data using sitewise mutation-selection models.
Genetics. 2012 Mar;190(3):1101-15. doi: 10.1534/genetics.111.136432. Epub 2011 Dec 29.
4
Mutation-selection models of coding sequence evolution with site-heterogeneous amino acid fitness profiles.
Proc Natl Acad Sci U S A. 2010 Mar 9;107(10):4629-34. doi: 10.1073/pnas.0910915107. Epub 2010 Feb 22.
5
Identifying changes in selective constraints: host shifts in influenza.
PLoS Comput Biol. 2009 Nov;5(11):e1000564. doi: 10.1371/journal.pcbi.1000564. Epub 2009 Nov 13.
6
Using non-homogeneous models of nucleotide substitution to identify host shift events: application to the origin of the 1918 'Spanish' influenza pandemic virus.
J Mol Evol. 2009 Oct;69(4):333-45. doi: 10.1007/s00239-009-9282-x. Epub 2009 Sep 29.
7
Evaluating the robustness of phylogenetic methods to among-site variability in substitution processes.
Philos Trans R Soc Lond B Biol Sci. 2008 Dec 27;363(1512):4013-21. doi: 10.1098/rstb.2008.0162.
8
Mutation-selection models of codon substitution and their use to estimate selective strengths on codon usage.
Mol Biol Evol. 2008 Mar;25(3):568-79. doi: 10.1093/molbev/msm284. Epub 2008 Jan 3.
9
Evolution in Mendelian Populations.
Genetics. 1931 Mar;16(2):97-159. doi: 10.1093/genetics/16.2.97.
10
Estimating the distribution of selection coefficients from phylogenetic data with applications to mitochondrial and viral DNA.
Mol Biol Evol. 2003 Aug;20(8):1231-9. doi: 10.1093/molbev/msg147. Epub 2003 May 30.
Zotero 插件